Impatiens is among the most diverse angiosperm genera, comprising more than 1000 species. The phylogenetic relationship among sections of Impatiens remains unclear. Plastomes and mitogenomes are useful for resolving problematic relationships in plant phylogenetics
however, conflicts between the organellar genomes have been reported. Here, we reconstructed the phylogeny of Impatiens using concatenated and multispecies coalescent (MSC) methods based on coding and noncoding regions of the plastome and coding regions of the mitogenome from 139 species, representing all major clades in Impatiens. Conflict analyses were conducted to test and visualize the incongruences between the organellar genomes and within the plastome. The analyses supported the monophyly of all subgenera and sections and identified a new clade (clade Longlinensis), but the relationships among these sections are inconsistent. There was incongruence between the organellar genome trees regarding the relationships among sect. Semeiocardium, sect. Racemosae and clade Longlinensis. There was also incongruence within the plastome regarding the relationships among sections Fasciculatae, Impatiens, Tuberosae, Scorpioidae, and Uniflorae. Our results show that incongruence between organellar genomes likely results from the complex evolutionary history of the genus, involving mixed inheritance of organellar genomes and hybridization. The incongruence within the plastome may result from the limited phylogenetic signal in plastome data, which could be due to the rapid radiation between 15.07 and 12.93 Ma. Specific genes and regions that led to such incongruence have been identified. By confirming the monophyly of Impatiens sections and detecting phylogenetic conflicts, this study provides a unique plastid and mitogenomic perspective on Impatiens phylogeny.